I have found a forum with a similar issue to what I am having except it was never responded to after the solution. I have a 2006 mustang gt with KNN CAI and Diablo Sport Predetor tuner. About a year ago, I was driving from back from Ohio to Wisconsin and noticed a "check charging sytem" message on the dash. There weren't many other symtoms. I stopped at a garage and it was charging only about 12.5 volts at an idle. I chose not to replace the alternator since it wasn't losing volts and was consistant. I made it back to Wisconsin and had very little (if any) issues for almost a year. This summer I have notice check charging system light coming on periodicially. Next, I noticed my fog lights would turn OFF for about 10 seconds along with dash lights coming ON for about 10 seconds. This would happen and go away for about a day or two. Now it seems to be happening more often. I am not going to drive it until I figure out what it is. Anyone who had the same or very similar problems please let me know a fix! I don't mind buying a part to fix it, but I don't want to throw money away if it is not the correct part.

THANK YOU!!

 

Replace the chronically marginal alternator with a PA Performance alt. These S197's have chronic issues with the alt and battery. One will take out the other.

12.5 volts alternator output at idle is a sure sign of a weak alternator. It should be about 13.2 volts, often higher.

 

check the smart junction box (passenger side kick panel) for water or corrosion).

If that yields nothing, check your charging system.